Alberto Contador rode the Giro with full knowledge that he was to answer to the Court of Arbitration for Sport (CAS) regarding his positive test for clenbuterol at the 2010 Tour de France, since his national federation cleared him of doping charges but both the UCI and the World Anti-Doping Agency (WADA) chose to appeal the ruling.[104][105] He rode and won with the most dominant Grand Tour performance of his career, and later rode a relatively normal and full 2011 season as his CAS date was continually pushed back. It was originally scheduled for June, to occur soon enough to decide conclusively his status prior to the 2011 Tour de France, but it was instead pushed back to August and then again to November.[106]

The hearing was at last held in November,[107] with a verdict expected in January 2012.[108] This, however, was also subject to a delay.[109] Finally, on 6 February 2012, the court spoke, overturning the Spanish federation's decision to clear Contador and assessing the rider a backdated two-year ban, from the date of his adverse test at the 2010 Tour de France. The backdated ban meant any results obtained from the time of that test to the time the court announced its verdict were to be vacated and awarded in turn to previously second-placed riders. This effectively made Michele Scarponi the new Giro champion and points winner, and it made José Rujano and Vincenzo Nibali into stage winners in this Giro.[110] The decision was reminiscent of that handed down in the Alessandro Petacchi case from the 2007 Giro d'Italia. The court's ruling opinion was that the minute amount of clenbuterol found was probably not caused by a doping regimen, but that strict liability rules meant that Contador had nonetheless violated WADA's World Anti-Doping Code. The court held that the adverse finding itself was never in doubt, but merely how the substance had entered the athlete's body. This was not a matter under which they could exonerate him.[111]

Reaction to the decision, and to the protracted nature of the case itself, was widespread and negative. Five-time Giro winner Eddy Merckx expressed surprise at the result and disappointment that it could further sully the sport's image, saying "It's like someone wants to kill cycling."[112] Since-ousted race director Angelo Zomegnan called the decision to strip the Giro championship "nonsense," noting that Contador was permitted to ride at the time and there were no irregularities of any kind during the race.[113] His successor Michele Acquarone was also upset by the decision, believing that damage had been done to the Giro and noting that RCS Sport would need to commission a new trophy to award to Scarponi.[114]

Scarponi, as well as John Gadret, the rider elevated onto the podium now in third place overall, both expressed sympathy for Contador and the feeling that being awarded these prestigious results in a court of law nearly a year after the race concluded kept them from feeling as good as they would were they attained on the road. Both Scarponi's overall championship and Gadret's podium finish constituted the first such results for either of them in a Grand Tour. Gadret, who had supported Contador's presence in the Giro peloton when the race began, reconsidered his position in hindsight, saying the Spaniard's attendance irrevocably changed the race.[115] Further reactions from other personalities within the sport toward the ruling and the case itself were near universally negative.[116][117][118][119][120][121] WADA celebrated the decision, calling the court "robust and thorough" in its jurisprudence of the World-Anti Doping Code.[119]